From 0329dc15b22c638ebf83a965e25f1f48609a5270 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <KrisThielemans@users.noreply.github.com>
Date: Mon, 1 Jul 2024 22:40:24 +0100
Subject: [PATCH 1/4] docker: use CMake 3.29.6

---
 docker/build_essential-ubuntu.sh | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/docker/build_essential-ubuntu.sh b/docker/build_essential-ubuntu.sh
index dbde1646..8d6e7c99 100755
--- a/docker/build_essential-ubuntu.sh
+++ b/docker/build_essential-ubuntu.sh
@@ -11,7 +11,6 @@ apt-get install -yq --no-install-recommends \
   g++             \
   gcc             \
   man             \
-  cmake           \
   ninja-build     \
   ccache          \
   sudo            \
@@ -21,10 +20,10 @@ apt-get clean
 pushd $INSTALL_DIR
 
 # CMake
-#curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.tar.gz
-#tar xzf cmake.tgz && rm cmake.tgz
-#ln -s cmake-*x86_64 cmake || true
-#export PATH="$PWD/cmake/bin:$PATH"
+curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.29.6/cmake-3.29.6-linux-x86_64.tar.gz
+tar xzf cmake.tgz && rm cmake.tgz
+ln -s cmake-*x86_64 cmake || true
+export PATH="$PWD/cmake/bin:$PATH"
 
 # ccache
 mkdir -p bin

From df6511064d4caed5a3cf5ff752610bae911936ba Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 2 Jul 2024 07:45:47 +0100
Subject: [PATCH 2/4] cmake in /usr/local

---
 docker/build_essential-ubuntu.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docker/build_essential-ubuntu.sh b/docker/build_essential-ubuntu.sh
index 8d6e7c99..7bc2bc8b 100755
--- a/docker/build_essential-ubuntu.sh
+++ b/docker/build_essential-ubuntu.sh
@@ -21,7 +21,11 @@ pushd $INSTALL_DIR
 
 # CMake
 curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.29.6/cmake-3.29.6-linux-x86_64.tar.gz
-tar xzf cmake.tgz && rm cmake.tgz
+mkdir -p /usr/local
+pushd /usr/local
+tar xzf $INSTALL_DIR/cmake.tgz --strip 1
+popd
+rm cmake.tgz
 ln -s cmake-*x86_64 cmake || true
 export PATH="$PWD/cmake/bin:$PATH"
 

From 5af0aaecba6c02e6cc0ba837f6f3af0bcee6964e Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <14138589+paskino@users.noreply.github.com>
Date: Tue, 2 Jul 2024 09:31:09 +0100
Subject: [PATCH 3/4] Disable Gadgetron CUDA build

---
 SuperBuild/External_Gadgetron.cmake | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index 94dbf0f5..d0aec05f 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -88,13 +88,15 @@ endif()
     "Build Gadgetron MATLAB gadgets (not required for SIRF)" ${default_Gadgetron_BUILD_MATLAB_SUPPORT})
   option(Gadgetron_USE_MKL "Instruct Gadgetron to build linking to the MKL. The user must be able to install MKL on his own." OFF)
 
+  # disable Gadgetron GPU code
+  set (${proj}_USE_CUDA OFF)
+  # TODO enable it once bug fixed
+  #if (USE_CUDA)
+  #  option(${proj}_USE_CUDA "Enable ${proj} CUDA" ${USE_CUDA})
+  #else()
+  #  set (${proj}_USE_CUDA OFF)
+  #endif()
   
-  if (USE_CUDA)
-    option(${proj}_USE_CUDA "Enable ${proj} CUDA" ${USE_CUDA})
-  else()
-    set (${proj}_USE_CUDA OFF)
-  endif()
-
   mark_as_advanced(${proj}_USE_CUDA)
 
   if (NOT DISABLE_OpenMP)

From 8e6824c89a043315fd2cd279eae656dc229f0db8 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 2 Jul 2024 09:45:26 +0000
Subject: [PATCH 4/4] minor review comments

---
 SuperBuild/External_Gadgetron.cmake | 2 +-
 VirtualBox/scripts/INSTALL_CMake.sh | 2 +-
 docker/build_essential-ubuntu.sh    | 2 --
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/SuperBuild/External_Gadgetron.cmake b/SuperBuild/External_Gadgetron.cmake
index d0aec05f..56854087 100644
--- a/SuperBuild/External_Gadgetron.cmake
+++ b/SuperBuild/External_Gadgetron.cmake
@@ -90,7 +90,7 @@ endif()
 
   # disable Gadgetron GPU code
   set (${proj}_USE_CUDA OFF)
-  # TODO enable it once bug fixed
+  # TODO enable after https://github.com/gadgetron/gadgetron/issues/1231
   #if (USE_CUDA)
   #  option(${proj}_USE_CUDA "Enable ${proj} CUDA" ${USE_CUDA})
   #else()
diff --git a/VirtualBox/scripts/INSTALL_CMake.sh b/VirtualBox/scripts/INSTALL_CMake.sh
index 9276454f..2c8f39ad 100755
--- a/VirtualBox/scripts/INSTALL_CMake.sh
+++ b/VirtualBox/scripts/INSTALL_CMake.sh
@@ -16,7 +16,7 @@ else
     INSTALL_LOC=$1
 fi
 # default version, but can be set externally
-: ${ver=3.21.3}
+: ${ver=3.29.6}
 
 echo "Downloading CMake $ver in /tmp"
 cd /tmp
diff --git a/docker/build_essential-ubuntu.sh b/docker/build_essential-ubuntu.sh
index 7bc2bc8b..8baf5b6f 100755
--- a/docker/build_essential-ubuntu.sh
+++ b/docker/build_essential-ubuntu.sh
@@ -26,8 +26,6 @@ pushd /usr/local
 tar xzf $INSTALL_DIR/cmake.tgz --strip 1
 popd
 rm cmake.tgz
-ln -s cmake-*x86_64 cmake || true
-export PATH="$PWD/cmake/bin:$PATH"
 
 # ccache
 mkdir -p bin